The MEME Suite

By Timothy L. Bailey, James Johnson, Charles E. Grant, William Stafford Noble. Nucleic Acids Res., 2015

4,336 citations recorded by the source corpus.

The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression. Since the previous description of the MEME Suite in the 2009 Nucleic Acids Research Web Server Issue, we have added six new tools. Here we describe the capabilities of all the tools within the suite, give advice on their best use and provide several case studies to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses. The MEME Suite is freely available for academic use at http://meme-suite.org, and source code is also available for download and local installation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e0b8531ec8e556ccb61fc9f70e9b00b1fc0ac2be

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Citations in the corpus

Maximum entropy methods for extracting the learned features of deep neural networks (2017, methodology): “3 (C) and (D), whenever FIMO called more than one motif in a sequence, we measured the distance between the network-derived motif and the FIMO motif with the lowest p-value.”
A new genome-mining tool redefines the lasso peptide biosynthetic landscape (2016, methodology): “Precursor peptide sequences from the training set (see above) were analyzed for the top 16 sequence motifs with zero or one occurrences per sequence using MEME (parameters: - nmotif 16 -mod zoops) 24 .”
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis (2017, methodology): “Major motif analysis software (14,45) include methods for motif finding, i.e., to detect occurrences of given motifs in a user-defined set of sequences of genomic regions.”
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins (2022, positive): “For de novo motif discovery or motif mapping, 500 bp flanking the top 1000 summits were sent for analysis using MEME suite (Bailey et al. 2015).”
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, methodology): “MEME datasets are used to visualize sequence motifs detected by the MEME suite (15).”
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors (2018, methodology): “The MEME Suite (40) was used to draw the logo of each TFBS (Figure 1D).”